Herein we highlight for the first time the ability to tune the stoichiometry of metal boride nanocrystals through nanoparticle synthesis in thermally stable inorganic molten salts. Two metal-boron systems are chosen as case studies: boron-poor nickel borides and boron-rich yttrium borides. We show that NiB, Ni4B3, Ni2B, Ni3B, and YB6 particles can be obtained as crystalline phases with good selectivity. Anisotropic crystallization is observed in two cases: the first boron-rich YB4 nanorods are reported, while boron-poor NiB nanoparticles show a peculiar crystal habit, as they are obtained as spheres with uniaxial defects related to the crystal structure. Crystallization mechanisms are proposed to account for the appearance of these two kinds of anisotropy at the nanoscale.